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Hoedt EC, Hueston CM, Cash N, Bongers RS, Keane JM, van Limpt K, Ben Amor K, Knol J, MacSharry J, van Sinderen D. A synbiotic mixture of selected oligosaccharides and bifidobacteria assists murine gut microbiota restoration following antibiotic challenge. Microbiome 2023; 11:168. [PMID: 37528457 PMCID: PMC10394833 DOI: 10.1186/s40168-023-01595-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/09/2023] [Indexed: 08/03/2023]
Abstract
BACKGROUND Typically, animal models studying gastrointestinal microbiotas compromised in early life have employed either germ-free animals or mice treated with a cocktail of antibiotics. Such studies intend to mimic scenarios of infants born by caesarean section and/or subjected to antibiotic treatment. However, the antibiotics used in these studies are rarely prescribed to infants. Therefore, an early life model was developed in which the murine gastrointestinal microbiota was severely disrupted by clindamycin treatment. RESULTS In this mouse model, we investigated the extent supplementation with a synbiotic mixture of prebiotics, being scGOS/lcFOS with the human milk oligosaccharide 2'-Fucosyllactose (2'-FL), in combination with or without single strain or mix of "infant type" bifidobacteria, can rescue an antibiotic-compromised microbiota. Shotgun metagenomic sequencing showed that the microbiota was severely disrupted by the clindamycin challenge. No recovery was observed 3 weeks post-challenge in the scGOS/lcFOS/2'FL group, while the group that received the synbiotic treatment of scGOS/lcFOS/2'-FL with Bifidobacterium breve NRBB01 showed partial recovery. Strikingly in the scGOS/lcFOS/2'-FL group receiving the mixture of bifidobacteria resulted in a recovery of the microbiota disruption. Histological analyses showed that the clindamycin-treated animals at the end of the experiment still suffered from mild oedema and villi/colonic crypt irregularities which was ameliorated by the synbiotic intervention. CONCLUSION Our study demonstrates that supplementation of synbiotic mixture of scGOS/lcFOS/2'-FL in combination with a specific mix of infant-type bifidobacterial strains is able to partially revive an antibiotic-perturbed gastrointestinal microbiota. Video Abstract.
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Affiliation(s)
- Emily C Hoedt
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
- Current address: NHMRC CRE in Digestive Health, HMRI, Newcastle, NSW, Australia
| | - Cara M Hueston
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Nora Cash
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | | | - Jonathan M Keane
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | | | | | - Jan Knol
- Danone Nutricia Research, Utrecht, The Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - John MacSharry
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland.
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.
- School of Medicine, University College Cork, Cork, Ireland.
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland.
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.
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Ortiz Camargo AR, van Mastrigt O, Bongers RS, Ben-Amor K, Knol J, Abee T, Smid EJ. Quantitative Physiology and Proteome Adaptations of Bifidobacterium breve NRBB57 at Near-Zero Growth Rates. Microbiol Spectr 2023; 11:e0256822. [PMID: 37184421 PMCID: PMC10269484 DOI: 10.1128/spectrum.02568-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 04/26/2023] [Indexed: 05/16/2023] Open
Abstract
In natural environments, nutrients are usually scarce, causing microorganisms to grow slowly while staying metabolically active. These natural conditions can be simulated using retentostat cultivations. The present study describes the physiological and proteome adaptations of the probiotic Bifidobacterium breve NRBB57 from high (0.4 h-1) to near-zero growth rates. Lactose-limited retentostat cultivations were carried out for 21 days in which the bacterial growth rate progressively reduced to 0.00092 h-1, leading to a 3.4-fold reduction of the maintenance energy requirement. Lactose was mainly converted into acetate, formate, and ethanol at high growth rates, while in the retentostat, lactate production increased. Interestingly, the consumption of several amino acids (serine, aspartic acid, and glutamine/arginine) and glycerol increased over time in the retentostat. Morphological changes and viable but nonculturable cells were also observed in the retentostat. Proteomes were compared for all growth rates, revealing a downregulation of ribosomal proteins at near-zero growth rates and an upregulation of proteins involved in the catabolism of alternative energy sources. Finally, we observed induction of the stringent response and stress defense systems. Retentostat cultivations were proven useful to study the physiology of B. breve, mimicking the nutrient scarcity of its complex habitat, the human gut. IMPORTANCE In natural environments, nutrients are usually scarce, causing microorganisms to grow slowly while staying metabolically active. In this study we used retentostat cultivation to investigate how the probiotic Bifidobacterium breve adapts its physiology and proteome under severe nutrient limitation resulting in near-zero growth rates (<0.001 h-1). We showed that the nutrient limitation induced a multifaceted response including stress defense and stringent response, metabolic shifts, and the activation of novel alternative energy-producing pathways.
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Affiliation(s)
| | - Oscar van Mastrigt
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | | | | | - Jan Knol
- Danone Nutricia Research, Utrecht, The Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Eddy J. Smid
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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3
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Camargo ARO, Van Mastrigt O, Bongers RS, Ben-Amor K, Knol J, Smid EJ, Abee T. Enhanced stress resistance of Bifidobacterium breve NRBB57 by induction of stress proteins at near-zero growth rates. Benef Microbes 2023; 14:85-94. [PMID: 36790092 DOI: 10.3920/bm2022.0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Bifidobacterium breve is a common habitant of the human gut and is used as probiotic in functional foods. B. breve has to cope with multiple stress conditions encountered during processing and passage through the human gut, including high temperature, low pH and exposure to oxygen. Additionally, during industrial processing and in the gut, B. breve could encounter nutrient limitation resulting in reduced growth rates that can trigger adaptive stress responses. For this reason, it is important to develop culture methods that elicit resistance to multiple stresses (robustness) encountered by the bacteria. To investigate the impact of caloric restriction on robustness of the probiotic B. breve NRBB57, this strain was grown in lactose-limited chemostat cultures and in retentostat for 21 days, at growth rates ranging from 0.4 h-1 to 0.00081 h-1. Proteomes of cells harvested at different growth rates were correlated to acid, hydrogen peroxide and heat stress survival capacity. Comparative proteome analysis showed that retentostat-grown cells had significantly increased abundance of a variety of stress proteins involved in protein quality maintenance and DNA repair (DnaJ, Hsp90, FtsH, ClpB, ClpP1, ClpC, GroES, RuvB, RecA), as well as proteins involved in oxidative stress defence (peroxiredoxin, ferredoxin, thioredoxin peroxidase, glutaredoxin and thioredoxin reductase). Exposure to three different stress conditions, 45 °C, pH 3, and 10 mM H2O2, showed highest stress resistance of retentostat cells sampled at week 2 and week 3 grown at 0.0018 and 0.00081 h-1. Our findings show that cultivation at near-zero growth rates induces higher abundance of stress defence proteins contributing to the robustness of B. breve NRBB57, thereby offering an approach that may support its production and functionality.
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Affiliation(s)
- A R Ortiz Camargo
- Food Microbiology, Wageningen University & Research, P.O. box 17, 6700 AA Wageningen, The Netherlands
| | - O Van Mastrigt
- Food Microbiology, Wageningen University & Research, P.O. box 17, 6700 AA Wageningen, The Netherlands
| | - R S Bongers
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, the Netherlands
| | - K Ben-Amor
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, the Netherlands
| | - J Knol
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, the Netherlands.,Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH Wageningen, the Netherlands
| | - E J Smid
- Food Microbiology, Wageningen University & Research, P.O. box 17, 6700 AA Wageningen, The Netherlands
| | - T Abee
- Food Microbiology, Wageningen University & Research, P.O. box 17, 6700 AA Wageningen, The Netherlands
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4
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Schimmel P, Kleinjans L, Bongers RS, Knol J, Belzer C. Breast milk urea as a nitrogen source for urease positive Bifidobacterium infantis. FEMS Microbiol Ecol 2021; 97:6128667. [PMID: 33538807 PMCID: PMC7947585 DOI: 10.1093/femsec/fiab019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/03/2021] [Indexed: 02/06/2023] Open
Abstract
Human milk stimulates a health-promoting gut microbiome in infants. However, it is unclear how the microbiota salvages and processes its required nitrogen from breast milk. Human milk nitrogen sources such as urea could contribute to the composition of this early life microbiome. Urea is abundant in human milk, representing a large part of the non-protein nitrogen (NPN). We found that B. longum subsp. infantis (ATCC17930) can use urea as a main source of nitrogen for growth in synthetic medium and enzyme activity was induced by the presence of urea in the medium. We furthermore confirmed the expression of both urease protein subunits and accessory proteins of B. longum subsp. infantis through proteomics. To the same end, metagenome data were mined for urease-related genes. It was found that the breastfed infant's microbiome possessed more urease-related genes than formula fed infants (51.4:22.1; 2.3-fold increase). Bifidobacteria provided a total of 106 of urease subunit alpha alignments, found only in breastfed infants. These experiments show how an important gut commensal that colonizes the infant intestine can metabolize urea. The results presented herein further indicate how dietary nitrogen can determine bacterial metabolism in the neonate gut and shape the overall microbiome.
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Affiliation(s)
- Patrick Schimmel
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Helix Building, 6708 WE, Wageningen, the Netherlands
| | - Lennart Kleinjans
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Helix Building, 6708 WE, Wageningen, the Netherlands
| | - Roger S Bongers
- Danone Nutricia Research, Uppsalalaan 12, 3584CT Utrecht, the Netherlands
| | - Jan Knol
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Helix Building, 6708 WE, Wageningen, the Netherlands.,Danone Nutricia Research, Uppsalalaan 12, 3584CT Utrecht, the Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Helix Building, 6708 WE, Wageningen, the Netherlands
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5
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Hoedt EC, Bottacini F, Cash N, Bongers RS, van Limpt K, Ben Amor K, Knol J, MacSharry J, van Sinderen D. Broad Purpose Vector for Site-Directed Insertional Mutagenesis in Bifidobacterium breve. Front Microbiol 2021; 12:636822. [PMID: 33833740 PMCID: PMC8021953 DOI: 10.3389/fmicb.2021.636822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/02/2021] [Indexed: 11/28/2022] Open
Abstract
Members of the genus Bifidobacterium are notoriously recalcitrant to genetic manipulation due to their extensive and variable repertoire of Restriction-Modification (R-M) systems. Non-replicating plasmids are currently employed to achieve insertional mutagenesis in Bifidobacterium. One of the limitations of using such insertion vectors is the presence within their sequence of various restriction sites, making them sensitive to the activity of endogenous restriction endonucleases encoded by the target strain. For this reason, vectors have been developed with the aim of methylating and protecting the vector using a methylase-positive Escherichia coli strain, in some cases containing a cloned bifidobacterial methylase. Here, we present a mutagenesis approach based on a modified and synthetically produced version of the suicide vector pORI28 (named pFREM28), where all known restriction sites targeted by Bifidobacterium breve R-M systems were removed by base substitution (thus preserving the codon usage). After validating the integrity of the erythromycin marker, the vector was successfully employed to target an α-galactosidase gene responsible for raffinose metabolism, an alcohol dehydrogenase gene responsible for mannitol utilization and a gene encoding a priming glycosyltransferase responsible for exopolysaccharides (EPS) production in B. breve. The advantage of using this modified approach is the reduction of the amount of time, effort and resources required to generate site-directed mutants in B. breve and a similar approach may be employed to target other (bifido)bacterial species.
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Affiliation(s)
- Emily C Hoedt
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | - Francesca Bottacini
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Nora Cash
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | | | | | | | - Jan Knol
- Danone Nutricia Research, Utrecht, Netherlands.,Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - John MacSharry
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,School of Microbiology, University College Cork, Cork, Ireland.,School of Medicine, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,School of Microbiology, University College Cork, Cork, Ireland
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Chia LW, Mank M, Blijenberg B, Bongers RS, van Limpt K, Wopereis H, Tims S, Stahl B, Belzer C, Knol J. Cross-feeding between Bifidobacterium infantis and Anaerostipes caccae on lactose and human milk oligosaccharides. Benef Microbes 2020; 12:69-83. [PMID: 33191780 DOI: 10.3920/bm2020.0005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The establishment of the gut microbiota immediately after birth is a dynamic process that may impact lifelong health. At this important developmental stage in early life, human milk oligosaccharides (HMOs) serve as specific substrates to shape the gut microbiota of the nursling. The well-orchestrated transition is important as an aberrant microbial composition and bacterial-derived metabolites are associated with colicky symptoms and atopic diseases in infants. Here, we study the trophic interactions between an HMO-degrader, Bifidobacterium infantis and the butyrogenic Anaerostipes caccae using carbohydrate substrates that are relevant in the early life period including lactose and total human milk carbohydrates. Mono- and co-cultures of these bacterial species were grown at pH 6.5 in anaerobic bioreactors supplemented with lactose or total human milk carbohydrates. A. caccae was not able to grow on these substrates except when grown in co-culture with B. infantis, leading to growth and concomitant butyrate production. Two levels of cross-feeding were observed, in which A. caccae utilised the liberated monosaccharides as well as lactate and acetate produced by B. infantis. This microbial cross-feeding points towards the key ecological role of bifidobacteria in providing substrates for other important species that will colonise the infant gut. The progressive shift of the gut microbiota composition that contributes to the gradual production of butyrate could be important for host-microbial crosstalk and gut maturation.
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Affiliation(s)
- L W Chia
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - M Mank
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands
| | - B Blijenberg
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands
| | - R S Bongers
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands
| | - K van Limpt
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands
| | - H Wopereis
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands
| | - S Tims
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands
| | - B Stahl
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands.,Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | - C Belzer
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - J Knol
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands.,Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands
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7
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Chia LW, Mank M, Blijenberg B, Aalvink S, Bongers RS, Stahl B, Knol J, Belzer C. Bacteroides thetaiotaomicron Fosters the Growth of Butyrate-Producing Anaerostipes caccae in the Presence of Lactose and Total Human Milk Carbohydrates. Microorganisms 2020; 8:E1513. [PMID: 33019531 PMCID: PMC7601031 DOI: 10.3390/microorganisms8101513] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/20/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022] Open
Abstract
The development of infant gut microbiota is strongly influenced by nutrition. Human milk oligosaccharides (HMOSs) in breast milk selectively promote the growth of glycan-degrading microbes, which lays the basis of the microbial network. In this study, we investigated the trophic interaction between Bacteroides thetaiotaomicron and the butyrate-producing Anaerostipes caccae in the presence of early-life carbohydrates. Anaerobic bioreactors were set up to study the monocultures of B. thetaiotaomicron and the co-cultures of B. thetaiotaomicron with A. caccae in minimal media supplemented with lactose or a total human milk carbohydrate fraction. Bacterial growth (qPCR), metabolites (HPLC), and HMOS utilization (LC-ESI-MS2) were monitored. B. thetaiotaomicron displayed potent glycan catabolic capability with differential preference in degrading specific low molecular weight HMOSs, including the neutral trioses (2'-FL and 3-FL), neutral tetraoses (DFL, LNT, LNnT), neutral pentaoses (LNFP I, II, III, V), and acidic trioses (3'-SL and 6'-SL). In contrast, A. caccae was not able to utilize lactose and HMOSs. However, the signature metabolite of A. caccae, butyrate, was detected in co-culture with B. thetaiotaomicron. As such, A. caccae cross-fed on B. thetaiotaomicron-derived monosaccharides, acetate, and d-lactate for growth and concomitant butyrate production. This study provides a proof of concept that B. thetaiotaomicron could drive the butyrogenic metabolic network in the infant gut.
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Affiliation(s)
- Loo Wee Chia
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (L.W.C.); (S.A.); (J.K.)
| | - Marko Mank
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (M.M.); (B.B.); (R.S.B.); (B.S.)
| | - Bernadet Blijenberg
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (M.M.); (B.B.); (R.S.B.); (B.S.)
| | - Steven Aalvink
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (L.W.C.); (S.A.); (J.K.)
| | - Roger S. Bongers
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (M.M.); (B.B.); (R.S.B.); (B.S.)
| | - Bernd Stahl
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (M.M.); (B.B.); (R.S.B.); (B.S.)
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Jan Knol
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (L.W.C.); (S.A.); (J.K.)
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (M.M.); (B.B.); (R.S.B.); (B.S.)
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (L.W.C.); (S.A.); (J.K.)
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8
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Ferrando ML, van Baarlen P, Orrù G, Piga R, Bongers RS, Wels M, De Greeff A, Smith HE, Wells JM. Carbohydrate availability regulates virulence gene expression in Streptococcus suis. PLoS One 2014; 9:e89334. [PMID: 24642967 PMCID: PMC3958366 DOI: 10.1371/journal.pone.0089334] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/17/2014] [Indexed: 12/04/2022] Open
Abstract
Streptococcus suis is a major bacterial pathogen of young pigs causing worldwide economic problems for the pig industry. S. suis is also an emerging pathogen of humans. Colonization of porcine oropharynx by S. suis is considered to be a high risk factor for invasive disease. In the oropharyngeal cavity, where glucose is rapidly absorbed but dietary α-glucans persist, there is a profound effect of carbohydrate availability on the expression of virulence genes. Nineteen predicted or confirmed S. suis virulence genes that promote adhesion to and invasion of epithelial cells were expressed at higher levels when S. suis was supplied with the α-glucan starch/pullulan compared to glucose as the single carbon source. Additionally the production of suilysin, a toxin that damages epithelial cells, was increased more than ten-fold when glucose levels were low and S. suis was growing on pullulan. Based on biochemical, bioinformatics and in vitro and in vivo gene expression studies, we developed a biological model that postulates the effect of carbon catabolite repression on expression of virulence genes in the mucosa, organs and blood. This research increases our understanding of S. suis virulence mechanisms and has important implications for the design of future control strategies including the development of anti-infective strategies by modulating animal feed composition.
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Affiliation(s)
- M. Laura Ferrando
- Host-Microbe Interactomics, Animal Sciences, Wageningen University, Wageningen, The Netherlands
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Peter van Baarlen
- Host-Microbe Interactomics, Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Germano Orrù
- Oral Biotechnology Laboratory, University of Cagliari, Cagliari, Italy
| | - Rosaria Piga
- Host-Microbe Interactomics, Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | | | | | - Astrid De Greeff
- Central Veterinary Institute, Animal Sciences Group, Wageningen University, Lelystad, The Netherlands
| | - Hilde E. Smith
- Central Veterinary Institute, Animal Sciences Group, Wageningen University, Lelystad, The Netherlands
| | - Jerry M. Wells
- Host-Microbe Interactomics, Animal Sciences, Wageningen University, Wageningen, The Netherlands
- * E-mail:
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9
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Van Bokhorst-van de Veen H, Bongers RS, Wels M, Bron PA, Kleerebezem M. Transcriptome signatures of class I and III stress response deregulation in Lactobacillus plantarum reveal pleiotropic adaptation. Microb Cell Fact 2013; 12:112. [PMID: 24238744 PMCID: PMC3842655 DOI: 10.1186/1475-2859-12-112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 11/11/2013] [Indexed: 01/17/2023] Open
Abstract
Background To cope with environmental challenges bacteria possess sophisticated defense mechanisms that involve stress-induced adaptive responses. The canonical stress regulators CtsR and HrcA play a central role in the adaptations to a plethora of stresses in a variety of organisms. Here, we determined the CtsR and HrcA regulons of the lactic acid bacterium Lactobacillus plantarum WCFS1 grown under reference (28°C) and elevated (40°C) temperatures, using ctsR, hrcA, and ctsR-hrcA deletion mutants. Results While the maximum specific growth rates of the mutants and the parental strain were similar at both temperatures (0.33 ± 0.02 h-1 and 0.34 ± 0.03 h-1, respectively), DNA microarray analyses revealed that the CtsR or HrcA deficient strains displayed altered transcription patterns of genes encoding functions involved in transport and binding of sugars and other compounds, primary metabolism, transcription regulation, capsular polysaccharide biosynthesis, as well as fatty acid metabolism. These transcriptional signatures enabled the refinement of the gene repertoire that is directly or indirectly controlled by CtsR and HrcA of L. plantarum. Deletion of both regulators, elicited transcriptional changes of a large variety of additional genes in a temperature-dependent manner, including genes encoding functions involved in cell-envelope remodeling. Moreover, phenotypic assays revealed that both transcription regulators contribute to regulation of resistance to hydrogen peroxide stress. The integration of these results allowed the reconstruction of CtsR and HrcA regulatory networks in L. plantarum, highlighting the significant intertwinement of class I and III stress regulons. Conclusions Taken together, our results enabled the refinement of the CtsR and HrcA regulatory networks in L. plantarum, illustrating the complex nature of adaptive stress responses in this bacterium.
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10
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Remus DM, van Kranenburg R, van Swam II, Taverne N, Bongers RS, Wels M, Wells JM, Bron PA, Kleerebezem M. Impact of 4 Lactobacillus plantarum capsular polysaccharide clusters on surface glycan composition and host cell signaling. Microb Cell Fact 2012; 11:149. [PMID: 23170998 PMCID: PMC3539956 DOI: 10.1186/1475-2859-11-149] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/08/2012] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Bacterial cell surface-associated polysaccharides are involved in the interactions of bacteria with their environment and play an important role in the communication between pathogenic bacteria and their host organisms. Cell surface polysaccharides of probiotic species are far less well described. Therefore, improved knowledge on these molecules is potentially of great importance to understand the strain-specific and proposed beneficial modes of probiotic action. RESULTS The Lactobacillus plantarum WCFS1 genome encodes 4 clusters of genes that are associated with surface polysaccharide production. Two of these clusters appear to encode all functions required for capsular polysaccharide formation (cps2A-J and cps4A-J), while the remaining clusters are predicted to lack genes encoding chain-length control functions and a priming glycosyl-transferase (cps1A-I and cps3A-J). We constructed L. plantarum WCFS1 gene deletion mutants that lack individual (Δcps1A-I, Δcps2A-J, Δcps3A-J and Δcps4A-J) or combinations of cps clusters (Δcps1A-3J and Δcps1A-3I, Δcps4A-J) and assessed the genome wide impact of these mutations by transcriptome analysis. The cps cluster deletions influenced the expression of variable gene sets in the individual cps cluster mutants, but also considerable numbers of up- and down-regulated genes were shared between mutants in cps cluster 1 and 2, as well as between mutant in cps clusters 3 and 4. Additionally, the composition of overall cell surface polysaccharide fractions was altered in each mutant strain, implying that despite the apparent incompleteness of cps1A-I and cps3A-J, all clusters are active and functional in L. plantarum. The Δcps1A-I strain produced surface polysaccharides in equal amounts as compared to the wild-type strain, while the polysaccharides were characterized by a reduced molar mass and the lack of rhamnose. The mutants that lacked functional copies of cps2A-J, cps3A-J or cps4A-J produced decreased levels of surface polysaccharides, whereas the molar mass and the composition of polysaccharides was not affected by these cluster mutations. In the quadruple mutant, the amount of surface polysaccharides was strongly reduced. The impact of the cps cluster mutations on toll-like receptor (TLR)-mediated human nuclear factor (NF)-κB activation in host cells was evaluated using a TLR2 reporter cell line. In comparison to a L. plantarum wild-type derivative, TLR2 activation remained unaffected by the Δcps1A-I and Δcps3A-J mutants but appeared slightly increased after stimulation with the Δcps2A-J and Δcps4A-J mutants, while the Δcps1A-3J and Δcps1A-3J, Δcps4A-J mutants elicited the strongest responses and clearly displayed enhanced TLR2 signaling. CONCLUSIONS Our study reveals that modulation of surface glycan characteristics in L. plantarum highlights the role of these molecules in shielding of cell envelope embedded host receptor ligands. Although the apparently complete cps clusters (cps2A-J and cps4A-J) contributed individually to this shielding, the removal of all cps clusters led to the strongest signaling enhancement. Our findings provide new insights into cell surface glycan biosynthesis in L. plantarum, which bears relevance in the context of host-cell signaling by probiotic bacteria.
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Affiliation(s)
- Daniela M Remus
- TI Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen,, The Netherlands
- NIZO food research, Kernhemseweg, 2, 6718 ZB Ede, The Netherlands
- Laboratory for Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | | | - Iris I van Swam
- TI Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen,, The Netherlands
- NIZO food research, Kernhemseweg, 2, 6718 ZB Ede, The Netherlands
| | - Nico Taverne
- TI Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen,, The Netherlands
- Host-Microbe Interactomics Group, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
| | - Roger S Bongers
- TI Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen,, The Netherlands
- NIZO food research, Kernhemseweg, 2, 6718 ZB Ede, The Netherlands
| | - Michiel Wels
- TI Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen,, The Netherlands
- NIZO food research, Kernhemseweg, 2, 6718 ZB Ede, The Netherlands
| | - Jerry M Wells
- TI Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen,, The Netherlands
- Host-Microbe Interactomics Group, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
| | - Peter A Bron
- TI Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen,, The Netherlands
- NIZO food research, Kernhemseweg, 2, 6718 ZB Ede, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, , 2600 GA Delft, The Netherlands
| | - Michiel Kleerebezem
- TI Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen,, The Netherlands
- NIZO food research, Kernhemseweg, 2, 6718 ZB Ede, The Netherlands
- Host-Microbe Interactomics Group, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
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Todt TJ, Wels M, Bongers RS, Siezen RS, van Hijum SAFT, Kleerebezem M. Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1. PLoS One 2012; 7:e45097. [PMID: 23028780 PMCID: PMC3447810 DOI: 10.1371/journal.pone.0045097] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 08/14/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In prokaryotes, sigma factors are essential for directing the transcription machinery towards promoters. Various sigma factors have been described that recognize, and bind to specific DNA sequence motifs in promoter sequences. The canonical sigma factor σ(70) is commonly involved in transcription of the cell's housekeeping genes, which is mediated by the conserved σ(70) promoter sequence motifs. In this study the σ(70)-promoter sequences in Lactobacillus plantarum WCFS1 were predicted using a genome-wide analysis. The accuracy of the transcriptionally-active part of this promoter prediction was subsequently evaluated by correlating locations of predicted promoters with transcription start sites inferred from the 5'-ends of transcripts detected by high-resolution tiling array transcriptome datasets. RESULTS To identify σ(70)-related promoter sequences, we performed a genome-wide sequence motif scan of the L. plantarum WCFS1 genome focussing on the regions upstream of protein-encoding genes. We obtained several highly conserved motifs including those resembling the conserved σ(70)-promoter consensus. Position weight matrices-based models of the recovered σ(70)-promoter sequence motif were employed to identify 3874 motifs with significant similarity (p-value<10(-4)) to the model-motif in the L. plantarum genome. Genome-wide transcript information deduced from whole genome tiling-array transcriptome datasets, was used to infer transcription start sites (TSSs) from the 5'-end of transcripts. By this procedure, 1167 putative TSSs were identified that were used to corroborate the transcriptionally active fraction of these predicted promoters. In total, 568 predicted promoters were found in proximity (≤ 40 nucleotides) of the putative TSSs, showing a highly significant co-occurrence of predicted promoter and TSS (p-value<10(-263)). CONCLUSIONS High-resolution tiling arrays provide a suitable source to infer TSSs at a genome-wide level, and allow experimental verification of in silico predicted promoter sequence motifs.
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Affiliation(s)
- Tilman J. Todt
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
- HAN University of Applied Sciences, Institute of Applied Sciences, Nijmegen, The Netherlands
| | - Michiel Wels
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
- NIZO food research, Ede, The Netherlands
- TI Food and Nutrition, Wageningen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
| | - Roger S. Bongers
- NIZO food research, Ede, The Netherlands
- TI Food and Nutrition, Wageningen, The Netherlands
| | - Roland S. Siezen
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
- HAN University of Applied Sciences, Institute of Applied Sciences, Nijmegen, The Netherlands
- NIZO food research, Ede, The Netherlands
- TI Food and Nutrition, Wageningen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
| | - Sacha A. F. T. van Hijum
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
- NIZO food research, Ede, The Netherlands
- TI Food and Nutrition, Wageningen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
- * E-mail:
| | - Michiel Kleerebezem
- NIZO food research, Ede, The Netherlands
- TI Food and Nutrition, Wageningen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Wageningen University, Host Microbe Interactomics Group, Wageningen, The Netherlands
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12
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Bron PA, Wels M, Bongers RS, van Bokhorst-van de Veen H, Wiersma A, Overmars L, Marco ML, Kleerebezem M. Transcriptomes reveal genetic signatures underlying physiological variations imposed by different fermentation conditions in Lactobacillus plantarum. PLoS One 2012; 7:e38720. [PMID: 22802930 PMCID: PMC3389018 DOI: 10.1371/journal.pone.0038720] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 05/14/2012] [Indexed: 01/04/2023] Open
Abstract
Lactic acid bacteria (LAB) are utilized widely for the fermentation of foods. In the current post-genomic era, tools have been developed that explore genetic diversity among LAB strains aiming to link these variations to differential phenotypes observed in the strains investigated. However, these genotype-phenotype matching approaches fail to assess the role of conserved genes in the determination of physiological characteristics of cultures by environmental conditions. This manuscript describes a complementary approach in which Lactobacillus plantarum WCFS1 was fermented under a variety of conditions that differ in temperature, pH, as well as NaCl, amino acid, and O2 levels. Samples derived from these fermentations were analyzed by full-genome transcriptomics, paralleled by the assessment of physiological characteristics, e.g., maximum growth rate, yield, and organic acid profiles. A data-storage and -mining suite designated FermDB was constructed and exploited to identify correlations between fermentation conditions and industrially relevant physiological characteristics of L. plantarum, as well as the associated transcriptome signatures. Finally, integration of the specific fermentation variables with the transcriptomes enabled the reconstruction of the gene-regulatory networks involved. The fermentation-genomics platform presented here is a valuable complementary approach to earlier described genotype-phenotype matching strategies which allows the identification of transcriptome signatures underlying physiological variations imposed by different fermentation conditions.
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Affiliation(s)
- Peter A. Bron
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
| | - Michiel Wels
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Roger S. Bongers
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
| | - Hermien van Bokhorst-van de Veen
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
- Laboratory of Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Anne Wiersma
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
| | - Lex Overmars
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Maria L. Marco
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
| | - Michiel Kleerebezem
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
- Laboratory of Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands
- Host-Microbe Interactomics, Wageningen University and Research Centre, Wageningen, The Netherlands
- * E-mail:
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Rud I, Naterstad K, Bongers RS, Molenaar D, Kleerebezem M, Axelsson L. Functional analysis of the role of CggR (central glycolytic gene regulator) in Lactobacillus plantarum by transcriptome analysis. Microb Biotechnol 2010; 4:345-56. [PMID: 21375718 PMCID: PMC3818993 DOI: 10.1111/j.1751-7915.2010.00223.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The level of the central glycolytic gene regulator (CggR) was engineered in Lactobacillus plantarum NC8 and WCFS1 by overexpression and in‐frame mutation of the cggR gene in order to evaluate its regulatory role on the glycolytic gap operon and the glycolytic flux. The repressor role of CggR on the gap operon was indicated through identification of a putative CggR operator and transcriptome analysis, which coincided with decreased growth rate and glycolytic flux when cggR was overexpressed in NC8 and WCFS1. The mutation of cggR did not affect regulation of the gap operon, indicating a more prominent regulatory role of CggR on the gap operon under other conditions than tested (e.g. fermentation of other sugars than glucose or ribose) and when the level of the putative effector molecule FBP is reduced. Interestingly, the mutation of cggR had several effects in NC8, i.e. increased growth rate and glycolytic flux and regulation of genes with functions associated with glycerol and pyruvate metabolism; however, no effects were observed in WCFS1. The affected genes in NC8 are presumably regulated by CcpA, since putative CRE sites were identified in their upstream regions. The interconnection with CggR and CcpA‐mediated control on growth and metabolism needs to be further elucidated.
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Affiliation(s)
- Ida Rud
- Nofima Mat, Osloveien 1, N-1430 Ås, Norway
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Marco ML, Peters THF, Bongers RS, Molenaar D, van Hemert S, Sonnenburg JL, Gordon JI, Kleerebezem M. Lifestyle of Lactobacillus plantarum in the mouse caecum. Environ Microbiol 2009; 11:2747-57. [PMID: 19638173 DOI: 10.1111/j.1462-2920.2009.02001.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lactobacillus plantarum is a common inhabitant of mammalian gastrointestinal tracts. Strains of L. plantarum are also marketed as probiotics intended to confer beneficial health effects upon delivery to the human gut. To understand how L. plantarum adapts to its gut habitat, we used whole genome transcriptional profiling to characterize the transcriptome of strain WCFS1 during colonization of the caeca of adult germ-free C57Bl/6 J mice fed a standard low-fat rodent chow diet rich in complex plant polysaccharides or a prototypic Western diet high in simple sugars and fat. Lactobacillus plantarum colonized the digestive tracts of these animals to high levels, although L. plantarum was found in 10-fold higher amounts in the caeca of mice fed the standard chow. Metabolic reconstructions based on the transcriptional data sets revealed that genes involved in carbohydrate transport and metabolism form the principal functional group that is upregulated in vivo compared with exponential phase cells grown in three different culture media, and that a Western diet provides a more nutritionally restricted, growth limiting milieu for the microbe in the distal gut. A set of bacterial genes encoding cell surface-related functions were differentially regulated in both groups of mice. This set included downregulated genes required for the d-alanylation of lipoteichoic acids, extracellular structures of L. plantarum that mediate interactions with the host immune system. These results, obtained in a reductionist gnotobiotic mouse model of the gut ecosystem, provide insights about the niches (professions) of this lactic acid bacterium, and a context for systematically testing features that affect epithelial and immune cell responses to this organism in the digestive tract.
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Affiliation(s)
- Maria L Marco
- TI Food and Nutrition, Nieuwe Kanaal 9A, 6709 PA, Wageningen, The Netherlands
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15
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Lambert JM, Bongers RS, de Vos WM, Kleerebezem M. Functional analysis of four bile salt hydrolase and penicillin acylase family members in Lactobacillus plantarum WCFS1. Appl Environ Microbiol 2008; 74:4719-26. [PMID: 18539794 PMCID: PMC2519332 DOI: 10.1128/aem.00137-08] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Accepted: 04/16/2008] [Indexed: 12/18/2022] Open
Abstract
Bile salts play an important role in the digestion of lipids in vertebrates and are synthesized and conjugated to either glycine or taurine in the liver. Following secretion of bile salts into the small intestine, intestinal microbes are capable of deconjugating the glycine or taurine from the bile salts, using an enzyme called bile salt hydrolase (Bsh). Intestinal lactobacilli are regarded as major contributors to bile salt hydrolysis in vivo. Since the bile salt-hydrolyzing strain Lactobacillus plantarum WCFS1 was predicted to carry four bsh genes (bsh1, bsh2, bsh3, and bsh4), the functionality of these bsh genes was explored using Lactococcus lactis heterologous overexpression and multiple bsh deletion strains. Thus, Bsh1 was shown to be responsible for the majority of Bsh activity in L. plantarum WCFS1. In addition, bsh1 of L. plantarum WCFS1 was shown to be involved in conferring tolerance to specific bile salts (i.e., glycocholic acid). Northern blot analysis established that bsh1, bsh2, bsh3, and bsh4 are all expressed in L. plantarum WCFS1 during the exponential growth phase. Following biodiversity analysis, bsh1 appeared to be the only bsh homologue that was variable among L. plantarum strains; furthermore, the presence of bsh1 correlated with the presence of Bsh activity, suggesting that Bsh1 is commonly responsible for Bsh activity in L. plantarum strains. The fact that bsh2, bsh3, and bsh4 genes appeared to be conserved among L. plantarum strains suggests an important role of these genes in the physiology and lifestyle of the species L. plantarum. Analysis of these additional bsh-like genes in L. plantarum WCFS1 suggests that they might encode penicillin acylase rather than Bsh activity, indicating their implication in the conversion of substrates other than bile acids in the natural habitat.
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Affiliation(s)
- Jolanda M Lambert
- TI Food & Nutrition, P.O. Box 557, 6700 AN Wageningen, The Netherlands
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Bron PA, Meijer M, Bongers RS, de Vos WM, Kleerebezem M. Dynamics of competitive population abundance of Lactobacillus plantarum ivi gene mutants in faecal samples after passage through the gastrointestinal tract of mice. J Appl Microbiol 2008; 103:1424-34. [PMID: 17953553 DOI: 10.1111/j.1365-2672.2007.03376.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AIM This study aims to evaluate the impact of mutation of previously identified in vivo-induced (ivi) genes on the persistence and survival of Lactobacillus plantarum WCFS1 in the gastrointestinal (GI) tract of mice. METHODS AND RESULTS Nine Lact. plantarum ivi gene replacement mutants were constructed, focussing on ivi genes that encode proteins with a predicted role in cell envelope functionality, stress response and regulation. The in vitro growth characteristics of the mutants appeared identical to those observed for the wild-type strain, which agrees with the recombination-based in vivo expression technology suggestion that these genes are not transcribed in the laboratory. Quantitative PCR experiments demonstrated differences in the relative population dynamics of the Lact. plantarum ivi mutants in faecal samples after passage through the GI tract of mice. CONCLUSIONS The in situ competition experiments revealed a 100- to 1000-fold reduction of the relative abundance of three of the ivi gene mutants, harbouring deletions of genes predicted to encode a copper transporter, an orphan IIC cellobiose PTS and a cell wall anchored extracellular protein. SIGNIFICANCE AND IMPACT OF THE STUDY These experiments clearly establish that the proteins encoded by these three genes play a key role in Lact. plantarum performance during passage of the GI tract.
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Affiliation(s)
- P A Bron
- Wageningen Centre for Food Sciences, Microbial Functionality and Safety Programme, Wageningen, The Netherlands
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Abstract
AIMS To assess which types of siderophores are typically produced by Brevibacterium and how siderophore production and utilization traits are distributed within this genus. METHODS AND RESULTS During co-cultivation experiments it was found that growth of B. linens Br5 was stimulated by B. linens NIZO B1410 by two orders of magnitude. The stimulation was caused by the production of hydroxamate siderophores by B. linens NIZO B1410 that enabled the siderophore-auxotrophic strain Br5 to grow faster under the applied iron-limited growth conditions. Different patterns of siderophore production and utilization were observed within the genus Brevibacterium. These patterns did not reflect the phylogenetic relations within the group as determined by partial 16S rDNA sequencing. Most Brevibacterium strains were found to utilize hydroxamate siderophores. CONCLUSIONS Brevibacteria can produce and utilize siderophores although certain strains within this genus are siderophore-auxotrophic. SIGNIFICANCE AND IMPACT OF THE STUDY It is reported for the first time that brevibacteria produce and utilize siderophores. This knowledge can be utilized to stimulate growth of auxotrophic strains under certain conditions. Enhancing the growth rate of Brevibacterium is of importance for the application of this species, for example, for cheese manufacturing or for industrial production of enzymes or metabolites.
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Lambert JM, Bongers RS, Kleerebezem M. Cre-lox-based system for multiple gene deletions and selectable-marker removal in Lactobacillus plantarum. Appl Environ Microbiol 2006; 73:1126-35. [PMID: 17142375 PMCID: PMC1828656 DOI: 10.1128/aem.01473-06] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The classic strategy to achieve gene deletion variants is based on double-crossover integration of nonreplicating vectors into the genome. In addition, recombination systems such as Cre-lox have been used extensively, mainly for eukaryotic organisms. This study presents the construction of a Cre-lox-based system for multiple gene deletions in Lactobacillus plantarum that could be adapted for use on gram-positive bacteria. First, an effective mutagenesis vector (pNZ5319) was constructed that allows direct cloning of blunt-end PCR products representing homologous recombination target regions. Using this mutagenesis vector, double-crossover gene replacement mutants could be readily selected based on their antibiotic resistance phenotype. In the resulting mutants, the target gene is replaced by a lox66-P(32)-cat-lox71 cassette, where lox66 and lox71 are mutant variants of loxP and P(32)-cat is a chloramphenicol resistance cassette. The lox sites serve as recognition sites for the Cre enzyme, a protein that belongs to the integrase family of site-specific recombinases. Thus, transient Cre recombinase expression in double-crossover mutants leads to recombination of the lox66-P(32)-cat-lox71 cassette into a double-mutant loxP site, called lox72, which displays strongly reduced recognition by Cre. The effectiveness of the Cre-lox-based strategy for multiple gene deletions was demonstrated by construction of both single and double gene deletions at the melA and bsh1 loci on the chromosome of the gram-positive model organism Lactobacillus plantarum WCFS1. Furthermore, the efficiency of the Cre-lox-based system in multiple gene replacements was determined by successive mutagenesis of the genetically closely linked loci melA and lacS2 in L. plantarum WCFS1. The fact that 99.4% of the clones that were analyzed had undergone correct Cre-lox resolution emphasizes the suitability of the system described here for multiple gene replacement and deletion strategies in a single genetic background.
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Affiliation(s)
- Jolanda M Lambert
- Wegeningen Centre for Food Science, Microbial Functionality and Safety Programme, Health and Safety Department, P.O. Box 20, 6710 BA Ede, The Netherlands
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Marco ML, Bongers RS, de Vos WM, Kleerebezem M. Spatial and temporal expression of Lactobacillus plantarum genes in the gastrointestinal tracts of mice. Appl Environ Microbiol 2006; 73:124-32. [PMID: 17071785 PMCID: PMC1797133 DOI: 10.1128/aem.01475-06] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactobacillus plantarum is a common inhabitant of mammalian gastrointestinal tracts, and L. plantarum strain WCFS1 is a human isolate with a known genome sequence. L. plantarum WCFS1 survives intestinal passage in an active form, and its transit time and transcriptional activities were monitored in 15 BALB/c mice at 2, 4, 6, 8, and 24 h after being fed a single intragastric dose of this organism. Enumeration of viable cells isolated from fecal material revealed that the majority of the L. plantarum inoculum transited the mouse intestine within 4 h after ingestion. Three mice were sacrificed at each time point, and total RNA was isolated from the mouse intestinal compartments (stomach through colon). Quantification of L. plantarum 16S rRNA by quantitative real-time reverse-transcription-PCR revealed that L. plantarum was present at elevated levels in the stomach and small intestine for at least 4 h following ingestion and for over 8 h in the cecum and colon. We also examined the expression of 9 L. plantarum housekeeping genes and 15 L. plantarum in vivo-inducible (ivi) genes previously identified by recombination-based in vivo expression technology to be induced in the mouse gastrointestinal tract. The relative expression levels of the ivi genes increased up to 350-fold in the mouse intestine compared to levels observed for L. plantarum WCFS1 cells grown in a rich laboratory medium. Moreover, several genes displayed intestinal compartment-specific (small intestine versus colon) activities. These results confirm that L. plantarum displays specific and differential responses at various sites along the mammalian intestine.
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Affiliation(s)
- Maria L Marco
- Wageningen Center for Food Sciences, NIZO food research, P.O. Box 20, 6710 BA Ede, The Netherlands
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Fu RY, Bongers RS, van Swam II, Chen J, Molenaar D, Kleerebezem M, Hugenholtz J, Li Y. Introducing glutathione biosynthetic capability into Lactococcus lactis subsp. cremoris NZ9000 improves the oxidative-stress resistance of the host. Metab Eng 2006; 8:662-71. [PMID: 16962352 DOI: 10.1016/j.ymben.2006.07.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2006] [Revised: 06/28/2006] [Accepted: 07/25/2006] [Indexed: 01/23/2023]
Abstract
This study describes how a metabolic engineering approach can be used to improve bacterial stress resistance. Some Lactococcus lactis strains are capable of taking up glutathione, and the imported glutathione protects this organism against H(2)O(2)-induced oxidative stress. L. lactis subsp. cremoris NZ9000, a model organism of this species that is widely used in the study of metabolic engineering, can neither synthesize nor take up glutathione. The study described here aimed to improve the oxidative-stress resistance of strain NZ9000 by introducing a glutathione biosynthetic capability. We show that the glutathione produced by strain NZ9000 conferred stronger resistance on the host following exposure to H(2)O(2) (150 mM) and a superoxide generator, menadione (30 microM). To explore whether glutathione can complement the existing oxidative-stress defense systems, we constructed a superoxide dismutase deficient mutant of strain NZ9000, designated as NZ4504, which is more sensitive to oxidative stress, and introduced the glutathione biosynthetic capability into this strain. Glutathione produced by strain NZ4504(pNZ3203) significantly shortens the lag phase of the host when grown aerobically, especially in the presence of menadione. In addition, cells of NZ4504(pNZ3203) capable of producing glutathione restored the resistance of the host to H(2)O(2)-induced oxidative stress, back to the wild-type level. We conclude that the resistance of L. lactis subsp. cremoris NZ9000 to oxidative stress can be increased in engineered cells with glutathione producing capability.
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Affiliation(s)
- Rui-Yan Fu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Southern Yangtze University, Wuxi 214036, People's Republic of China
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Bongers RS, Veening JW, Van Wieringen M, Kuipers OP, Kleerebezem M. Development and characterization of a subtilin-regulated expression system in Bacillus subtilis: strict control of gene expression by addition of subtilin. Appl Environ Microbiol 2006; 71:8818-24. [PMID: 16332878 PMCID: PMC1317459 DOI: 10.1128/aem.71.12.8818-8824.2005] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A system for subtilin-regulated gene expression (SURE) in Bacillus subtilis that is based on the regulatory module involved in cell-density-dependent control of the production of subtilin is described. An integration vector for introduction of the essential sensor-regulator couple spaRK into the amyE locus of the B. subtilis chromosome and a B. subtilis 168-derived production host in which the spaRK genes were functionally introduced were constructed. Furthermore, several expression plasmids harboring the subtilin-inducible wild-type spaS promoter or a mutated derivative of this promoter were constructed, which facilitated both transcriptional and translational promoter-gene fusions. Functional characterization of both spaS promoters and the cognate expression host could be performed by controlled overproduction of the beta-glucuronidase (GusA) and green fluorescent protein (GFP) reporters. Both spaS promoters exhibited very low levels of basal expression, while extremely high levels of expression were observed upon induction with subtilin. Moreover, the level of expression depended directly on the amount of inducer (subtilin) used. The wild-type spaS promoter appeared to be more strictly controlled by the addition of subtilin, while the highest levels of expression were obtained when the mutated spaS promoter was used. Induction by subtilin led to 110- and 80-fold increases in GusA activity for the spaS promoter and its mutant derivative, respectively. Since the SURE system has attractive functional characteristics, including promoter silence under noninducing conditions and a controlled and high level of expression upon induction, and since it is not subject to catabolite control, we anticipate that it can provide a suitable expression system for various scientific and industrial applications.
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Affiliation(s)
- Roger S Bongers
- NIZO food research, Department of Health and Safety, P.O. Box 20, 6710 BA Ede, The Netherlands.
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Abstract
Efficient conversion of glucose to acetaldehyde is achieved by nisin-controlled overexpression of Zymomonas mobilis pyruvate decarboxylase (pdc) and Lactococcus lactis NADH oxidase (nox) in L. lactis. In resting cells, almost 50% of the glucose consumed could be redirected towards acetaldehyde by combined overexpression of pdc and nox under anaerobic conditions.
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Affiliation(s)
- Roger S Bongers
- NIZO food research, Department of Flavour and Natural Ingredients, P.O. Box 20, 6710 BA Ede, The Netherlands.
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Bongers RS, Hoefnagel MHN, Starrenburg MJC, Siemerink MAJ, Arends JGA, Hugenholtz J, Kleerebezem M. IS981-mediated adaptive evolution recovers lactate production by ldhB transcription activation in a lactate dehydrogenase-deficient strain of Lactococcus lactis. J Bacteriol 2003; 185:4499-507. [PMID: 12867459 PMCID: PMC165757 DOI: 10.1128/jb.185.15.4499-4507.2003] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis NZ9010 in which the las operon-encoded ldh gene was replaced with an erythromycin resistance gene cassette displayed a stable phenotype when grown under aerobic conditions, and its main end products of fermentation under these conditions were acetate and acetoin. However, under anaerobic conditions, the growth of these cells was strongly retarded while the main end products of fermentation were acetate and ethanol. Upon prolonged subculturing of this strain under anaerobic conditions, both the growth rate and the ability to produce lactate were recovered after a variable number of generations. This recovery was shown to be due to the transcriptional activation of a silent ldhB gene coding for an Ldh protein (LdhB) with kinetic parameters different from those of the native las operon-encoded Ldh protein. Nevertheless, cells producing LdhB produced mainly lactate as the end product of fermentation. The mechanism underlying the ldhB gene activation was primarily studied in a single-colony isolate of the recovered culture, designated L. lactis NZ9015. Integration of IS981 in the upstream region of ldhB was responsible for transcription activation of the ldhB gene by generating an IS981-derived -35 promoter region at the correct spacing with a natively present -10 region. Subsequently, analysis of 10 independently isolated lactate-producing derivatives of L. lactis NZ9010 confirmed that the ldhB gene is transcribed in all of them. Moreover, characterization of the upstream region of the ldhB gene in these derivatives indicated that site-specific and directional IS981 insertion represents the predominant mechanism of the observed recovery of the ability to produce lactate.
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Affiliation(s)
- Roger S Bongers
- Wageningen Centre for Food Sciences, NIZO Food Research, FNI Department, 6710 BA Ede, The Netherlands
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van Kraaij C, Breukink E, Rollema HS, Bongers RS, Kosters HA, de Kruijff B, Kuipers OP. Engineering a disulfide bond and free thiols in the lantibiotic nisin Z. Eur J Biochem 2000; 267:901-9. [PMID: 10651829 DOI: 10.1046/j.1432-1327.2000.01075.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The antimicrobial peptide nisin contains the uncommon amino acid residues lanthionine and methyl-lanthionine, which are post-translationally formed from Ser, Thr and Cys residues. To investigate the importance of these uncommon residues for nisin activity, a mutant was designed in which Thr13 was replaced by a Cys residue, which prevents the formation of the thioether bond of ring C. Instead, Cys13 couples with Cys19 via an intramolecular disulfide bridge, a bond that is very unusual in lantibiotics. NMR analysis of this mutant showed a structure very similar to that of wild-type nisin, except for the configuration of ring C. The modification was accompanied by a dramatic reduction in antimicrobial activity to less than 1% of wild-type activity, indicating that the lanthionine of ring C is very important for this activity. The nisin Z mutants S5C and M17C were also isolated and characterized; they are the first lantibiotics known that contain an additional Cys residue that is not involved in bridge formation but is present as a free thiol. Secretion of these peptides by the lactococcal producer cells, as well as their antimicrobial activity, was found to be strongly dependent on a reducing environment. Their ability to permeabilize lipid vesicles was not thiol-dependent. Labeling of M17C nisin Z with iodoacetamide abolished the thiol-dependence of the peptide. These results show that the presence of a reactive Cys residue in nisin has a strong effect on the antimicrobial properties of the peptide, which is probably the result of interaction of these residues with thiol groups on the outside of bacterial cells.
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Affiliation(s)
- C van Kraaij
- NIZO Food Research, Section Flavours and Natural Ingredients, Ede, The Netherlands.
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